Systems Biology under heat stress in Indian Cattle

AbstractTranscriptome profiling of Vrindavani and Tharparkar cattle revealed that more numbers of genes dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.5 % of upregulated genes in Vrindavani were downregulated in Tharparkar and 17.5% upregulated genes in Tharparkar were downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, and UBE2H) of misfolded proteins but also with protectors (VCP, Serp1, and CALR) of naïve unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.

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Transcriptome profiling and gene expression analyses of eggplant (Solanum melongena L.) under heat stress

PLoS ONE ◽

10.1371/journal.pone.0236980 ◽

2020 ◽

Vol 15 (8) ◽

pp. e0236980

Author(s):

Aidong Zhang ◽

Zongwen Zhu ◽

Jing Shang ◽

Shengmei Zhang ◽

Haibin Shen ◽

...

Keyword(s):

Gene Expression ◽

Heat Stress ◽

Solanum Melongena ◽

Transcriptome Profiling ◽

Gene Expression Analyses

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Systems Biology under heat stress in Indian Cattle

Gene ◽

10.1016/j.gene.2021.145908 ◽

2021 ◽

pp. 145908

Author(s):

Raja Ishaq Nabi Khan ◽

Amit Ranjan Sahu ◽

Waseem Akram Malla ◽

Manas Ranjan Praharaj ◽

Neelima Hosamani ◽

...

Keyword(s):

Heat Stress ◽

Systems Biology ◽

Indian Cattle

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Flavonoids improve drought tolerance of maize seedlings by regulating the homeostasis of reactive oxygen species

Plant and Soil ◽

10.1007/s11104-020-04814-8 ◽

2021 ◽

Author(s):

Baozhu Li ◽

Ruonan Fan ◽

Guiling Sun ◽

Ting Sun ◽

Yanting Fan ◽

...

Keyword(s):

Free Radicals ◽

Drought Stress ◽

Drought Tolerance ◽

Infrared Imaging ◽

Oxygen Free Radicals ◽

Transcriptome Profiling ◽

Far Infrared ◽

Drought Treatment ◽

Physiological Characterization ◽

Oxidative Damages

Abstract Background and aims As drought threatens the yield and quality of maize (Zea mays L.), it is important to dissect the molecular basis of maize drought tolerance. Flavonoids, participate in the scavenging of oxygen free radicals and alleviate stress-induced oxidative damages. This study aims to dissect the function of flavonoids in the improvement of maize drought tolerance. Methods Using far-infrared imaging screening, we previously isolated a drought overly insensitivity (doi) mutant from an ethyl methanesulfonate (EMS)-mutagenized maize library and designated it as doi57. In this study, we performed a physiological characterization and transcriptome profiling of doi57 in comparison to corresponding wild-type B73 under drought stress. Results Under drought stress, doi57 seedlings displayed lower leaf-surface temperature (LST), faster water loss, and better performance in growth than B73. Transcriptome analysis reveals that key genes involved in flavonoid biosynthesis are enriched among differentially expressed genes in doi57. In line with these results, more flavonols and less hydrogen peroxide (H2O2) were accumulated in guard cells of doi57 than in those of B73 with the decrease of soil water content (SWC). Moreover, the capacity determined from doi57 seedling extracts to scavenge oxygen free radicals was more effective than that of B73 under the drought treatment. Additionally, doi57 seedlings had higher photosynthetic rates, stomatal conductance, transpiration rates, and water use efficiency than B73 exposed to drought stress, resulting in high biomass and greater root/shoot ratios in doi57 mutant plants. Conclusion Flavonoids may facilitate maize seedling drought tolerance by lowering drought-induced oxidative damage as well regulating stomatal movement.

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Gene Expression and Carcass Traits Are Different between Different Quality Grade Groups in Red-Faced Hereford Steers

Animals ◽

10.3390/ani11071910 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1910

Author(s):

Bailey Engle ◽

Molly Masters ◽

Jane Ann Boles ◽

Jennifer Thomson

Keyword(s):

Gene Expression ◽

Transcriptome Profiling ◽

Fat Deposition ◽

Lower Shear ◽

The Us ◽

Quality Grade ◽

Longissimus Lumborum ◽

Muscle Biochemistry ◽

Marbling Deposition ◽

Insight Into

Fat deposition is important to carcass value and some palatability characteristics. Carcasses with higher USDA quality grades produce more value for producers and processors in the US system and are more likely to have greater eating satisfaction. Using genomics to identify genes impacting marbling deposition provides insight into muscle biochemistry that may lead to ways to better predict fat deposition, especially marbling and thus quality grade. Hereford steers (16) were managed the same from birth through harvest after 270 days on feed. Samples were obtained for tenderness and transcriptome profiling. As expected, steaks from Choice carcasses had a lower shear force value than steaks from Select carcasses; however, steaks from Standard carcasses were not different from steaks from Choice carcasses. A significant number of differentially expressed (DE) genes was observed in the longissimus lumborum between Choice and Standard carcass RNA pools (1257 genes, p < 0.05), but not many DE genes were observed between Choice and Select RNA pools. Exploratory analysis of global muscle tissue transcriptome from Standard and Choice carcasses provided insight into muscle biochemistry, specifically the upregulation of extracellular matrix development and focal adhesion pathways and the downregulation of RNA processing and metabolism in Choice versus Standard. Additional research is needed to explore the function and timing of gene expression changes.

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Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract

Scientific Reports ◽

10.1038/s41598-021-81611-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rupalatha Maddala ◽

Junyuan Gao ◽

Richard T. Mathias ◽

Tylor R. Lewis ◽

Vadim Y. Arshavsky ◽

...

Keyword(s):

Calcium Binding ◽

Late Onset ◽

Cpg Islands ◽

Transcriptome Profiling ◽

Specific Gene ◽

Pathway Network ◽

S100a4 Expression ◽

Histone H3k27 ◽

Pathway Analyses ◽

Upregulated Genes

AbstractS100A4, a member of the S100 family of multifunctional calcium-binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in differentiating fiber cells of the ocular lens and that S100A4(−/−) knockout mice develop late-onset cortical cataracts. Transcriptome profiling of lenses from S100A4(−/−) mice revealed a robust increase in the expression of multiple photoreceptor- and Müller glia-specific genes, as well as the olfactory sensory neuron-specific gene, S100A5. This aberrant transcriptional profile is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of differentially expressed genes in S100A4(−/−) lenses identified Crx and Nrl transcription factors as the most significant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high-density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this finding, we further documented that S100A4(−/−) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together, our findings suggest that S100A4 suppresses the expression of retinal genes during lens differentiation plausibly via a mechanism involving changes in histone methylation.

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